Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2.

Genomic epidemiology is important to study the COVID-19 pandemic, and more than two million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequences were deposited into public databases. However, the exponential increase of sequences invokes unprecedented bioinformatic challenges. Here, we present the Coronavirus GenBrowser (CGB) based on a highly efficient analysis framework and a node-picking rendering strategy. In total, 1,002,739 high-quality genomic sequences with the transmission-related metadata were analyzed and visualized. The size of the core data file is only 12.20 MB, highly efficient for clean data sharing. Quick visualization modules and rich interactive operations are provided to explore the annotated SARS-CoV-2 evolutionary tree. CGB binary nomenclature is proposed to name each internal lineage. The pre-analyzed data can be filtered out according to the user-defined criteria to explore the transmission of SARS-CoV-2. Different evolutionary analyses can also be easily performed, such as the detection of accelerated evolution and ongoing positive selection. Moreover, the 75 genomic spots conserved in SARS-CoV-2 but non-conserved in other coronaviruses were identified, which may indicate the functional elements specifically important for SARS-CoV-2. The CGB was written in Java and JavaScript. It not only enables users who have no programming skills to analyze millions of genomic sequences, but also offers a panoramic vision of the transmission and evolution of SARS-CoV-2.

Precision tailoring of laser beam propagation in a single crystalline diamond tool for in situ laser-assisted diamond turning.

The characteristics of laser beam propagation within a diamond tool critically influence the applied thermal softening capability of in situ laser-assisted diamond turning (In-LAT). In the present work, we perform optical geometric analysis, optical simulation and experimental validation to propose a novel diamond tool configuration for precisely tailoring laser beam propagation in In-LAT. First, the characteristics of laser beam propagation in the current In-LAT diamond tool are theoretically and experimentally explored. Second, according to the issues discovered in the current In-LAT diamond tool, an improved tool configuration based on the total internal reflection of a laser beam within the diamond tool is proposed, aiming for promoting refraction of the laser beam from the rake face of the diamond tool as well as eliminating the reflection of laser beam to tool holder. Finally, the optimization of laser beam incident position is carried out for achieving the superior profile and intensity of the emitted laser spot. Current work provides rational laser beam propagation for improving the thermal-softening capability of an In-LAT diamond tool.

Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition.

Population size history is essential for studying human evolution. However, ancient population size history during the Pleistocene is notoriously difficult to unravel. In this study, we developed a fast infinitesimal time coalescent process (FitCoal) to circumvent this difficulty and calculated the composite likelihood for present-day human genomic sequences of 3154 individuals. Results showed that human ancestors went through a severe population bottleneck with about 1280 breeding individuals between around 930,000 and 813,000 years ago. The bottleneck lasted for about 117,000 years and brought human ancestors close to extinction. This bottleneck is congruent with a substantial chronological gap in the available African and Eurasian fossil record. Our results provide new insights into our ancestry and suggest a coincident speciation event.

Design and Implementation of Ultrasonic Impact Peening-Based Device for Stainless Steel Surface Texture Fabrication.

The manufacturing of precise surface microstructures with low cost is needed for surface texturing-based surface engineering. In this paper, a device for the fabrication of surface microgroove texture on stainless steel based on ultrasonic impact peening (UIP) is proposed and investigated. First, the principle of applying the UIP into the fabrication of surface texture is analytically described. Then, the design of the UIP device, particularly the design of functional systems and mechanical structures, is carried out. Next, a UIP experimental device is built, and is further applied to fabricate microgroove textures on 316L stainless steel. The subsequent experimental characterization of microgroove morphology demonstrates the feasibility of the designed UIP device for the fabrication of stainless steel surface texture.

New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era.

Genetic recombination is a very important evolutionary mechanism that mixes parental haplotypes and produces new raw material for organismal evolution. As a result, information on recombination rates is critical for biological research. In this paper, we introduce a new extremely fast open-source software package (FastEPRR) that uses machine learning to estimate recombination rate [Formula: see text] (=[Formula: see text]) from intraspecific DNA polymorphism data. When [Formula: see text] and the number of sampled diploid individuals is large enough ([Formula: see text]), the variance of [Formula: see text] remains slightly smaller than that of [Formula: see text] The new estimate [Formula: see text] (calculated by averaging [Formula: see text] and [Formula: see text]) has the smallest variance of all cases. When estimating [Formula: see text], the finite-site model was employed to analyze cases with a high rate of recurrent mutations, and an additional method is proposed to consider the effect of variable recombination rates within windows. Simulations encompassing a wide range of parameters demonstrate that different evolutionary factors, such as demography and selection, may not increase the false positive rate of recombination hotspots. Overall, accuracy of FastEPRR is similar to the well-known method, LDhat, but requires far less computation time. Genetic maps for each human population (YRI, CEU, and CHB) extracted from the 1000 Genomes OMNI data set were obtained in less than 3 d using just a single CPU core. The Pearson Pairwise correlation coefficient between the [Formula: see text] and [Formula: see text] maps is very high, ranging between 0.929 and 0.987 at a 5-Mb scale. Considering that sample sizes for these kinds of data are increasing dramatically with advances in next-generation sequencing technologies, FastEPRR (freely available at http://www.picb.ac.cn/evolgen/) is expected to become a widely used tool for establishing genetic maps and studying recombination hotspots in the population genomic era.